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. 2023 Jan 2;7(2):264–278. doi: 10.1038/s41559-022-01925-6

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 4 — a, Computational pipeline for de novo gene identification. (b-d) The distributions of GC content (b, n = 21,392 for protein-coding genes; n = 74 for de novo genes; n = 7,109 for lncRNA loci; one-sided, unpaired Wilcoxon test, P value = 5.5e-3 and P value < 2.2e-16, respectively), N/C ratio (c, n = 15,734 for protein-coding genes; n = 33 for de novo genes; n = 1,860 for lncRNA loci; one-sided, unpaired Wilcoxon test, P value = 0.40, 0.16, respectively), and ISOR (d, two-sided, unpaired Wilcoxon test, P value < 2.2e-16, 0.94, respectively), for de novo genes (De novo, n = 61), protein-coding genes (Protein-coding, n = 17,990) and genes encoding lncRNAs (LncRNAs, n = 2,777). The boxes represent interquartile range, with the line across the box indicates the median. The whiskers extend to the lowest and the highest value in the dataset. e, The number of de novo genes co-opting with the transcriptional context of cis-NATs (Natural Antisense Transcripts) or bi-directional promoters were summarized and shown in pieplot. bi: bi-directional promoters; +: overlapping with known genes of same strand; -: overlapping with known genes of reverse strand. Here ‘overlapping a known gene’ means coordinate overlap, rather than an overlap with a known gene in the same frame. f, The distributions of the length of proteins, for de novo genes and protein-coding genes. g, The distributions of the expression levels for de novo genes, protein-coding genes and genes encoding lncRNAs. **P value ≤ 0.01; ***P value ≤ 0.001; N.S, not significant.